MolNFT v1 · #141185 · protein

Crystal structure of human crmp-2 with T509D-T514D-S518D-S522D mutations

5YZ5 · Dihydropyrimidinase-related protein 2: “Crystal structure of human crmp-2 with T509D-T514D-S518D-S522D mutations”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.63). MolNFT v1 #141185 on GenesisL1: 3D structure…

PDB: 5YZ5
Type: protein
Length: 492 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydropyrimidinase-related protein 2
UniProt: Q16555
Ligands: SO4
Pockets: 2 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dihydropyrimidinase-related protein 2	protein	492	35% helix, 23% strand	Q16555

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	247	0.63	0.81	37	empty
2	164	0.62	0.84	20	empty

Compared structures

5YZ5 · Crystal Structure of Human CRMP-2 with T509D-T514D-S518D-S522D mutations · the same entry in another collection · chain A against A, TM-score 1.00
Q16555 · AlphaFold monomer V2.0 prediction for dihydropyrimidinase-related protein 2 (Q16555) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q16555
Elsewhere: RCSB PDB 5YZ5 · PDBe 5YZ5 · UniProt Q16555

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